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Question: Question: What is the difference between _c and rep_c types of consensus sequences in MIRA?

Abhimanyu Singh
39 days ago

Question: What is the difference between _c and rep_c types of consensus sequences in MIRA?

MIRA produces contigs with varied names:

1)>projName_c[number] 2)>projName_rep_c[number]

What is the difference between these two types of consensus sequences?

Answers
0

MIRA names contigs the following way: <projectname>_<contigtype><number>. While <projectname> is dictated by the [--project=] parameter and <number> should be clear, the <contigtype> might need additional explaining. There are currently three contig types existing:

  1. _c: these are "normal" contigs

  2. _rep_c: these are contigs containing only repetitive areas. These contigs had _lrc as type in previous version of MIRA, this was changed to the _rep_c to make things clearer.

  3. _s: these are singlet-contigs. Technically: "contigs" with a single read.

  4. _dn: these is an additional contig type which can occur when MIRA ran a digital normalisation step during the assembly. Contigs which contain reads completely covered by a DGNr tag will get an additional "_dn" as part of their name to show that they contain read representatives for digital normalisation. E.g.: "contig_dn_c1" or "contig_dn_rep_c2".

source @ http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html